Asian seabass (Lates calcarifer) undergoes a male-to-female sex change but the molecular mechanisms regulating the process are poorly understood. In this study, custom genomic platforms were generated to analyze the process. A mid-throughput qPCR analysis of the various testicular and ovarian maturation stages showed that the expression profiles of 36 genes were sufficient to identify the testes and ovaries irrespective of the maturation stage. In addition, distinctive expression profiles and markers characteristic of specific stages were discovered. Subsequently, microarray analysis showed that during sex change, pro-male genes were down-regulated while apoptosis was activated. The early transforming gonads hence returned to a near-undifferentiated transcriptomic state before ovarian differentiation involving processes such as Wnt/beta-catenin signaling took place. The role of Wnt/beta-catenin signaling in promoting ovarian differentiation was functionally validated using transgenic zebrafish. These findings reinforced the current notion that sex differentiation is conserved in vertebrates and showed that the pro-male and pro-female processes involved in testis-to-ovary or ovary-to-testis sex change remain the same albeit in the opposite direction.